Open Access
Identifying and removing haplotypic duplication in primary genome assemblies
Dengfeng Guan
1, 2
,
Susan A. MaCarthy
2
,
Kerstin Howe
3
,
Richard L. Durbin
2, 3
,
Jonathan Wood
3
,
Yadong Wang
1
Publication type: Journal Article
Publication date: 2020-01-23
scimago Q1
wos Q1
SJR: 2.451
CiteScore: 9.6
Impact factor: 5.4
ISSN: 13674803, 13674811, 14602059
PubMed ID:
31971576
Biochemistry
Computer Science Applications
Molecular Biology
Statistics and Probability
Computational Mathematics
Computational Theory and Mathematics
Abstract
Motivation
Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. Several tools have been developed to resolve this problem. However, they either focus only on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors.
Results
Here we present a novel tool, purge_dups, that uses sequence similarity and read depth to automatically identify and remove both haplotigs and heterozygous overlaps. In comparison with current tools, we demonstrate that purge_dups can reduce heterozygous duplication and increase assembly continuity while maintaining completeness of the primary assembly. Moreover, purge_dups is fully automatic and can easily be integrated into assembly pipelines.
Availability and implementation
The source code is written in C and is available at https://github.com/dfguan/purge_dups.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Cite this
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GOST
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Guan D. et al. Identifying and removing haplotypic duplication in primary genome assemblies // Bioinformatics. 2020. Vol. 36. No. 9. pp. 2896-2898.
GOST all authors (up to 50)
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Guan D., MaCarthy S. A., Howe K., Durbin R. L., Wood J., Wang Y. Identifying and removing haplotypic duplication in primary genome assemblies // Bioinformatics. 2020. Vol. 36. No. 9. pp. 2896-2898.
Cite this
RIS
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TY - JOUR
DO - 10.1093/bioinformatics/btaa025
UR - https://doi.org/10.1093/bioinformatics/btaa025
TI - Identifying and removing haplotypic duplication in primary genome assemblies
T2 - Bioinformatics
AU - Guan, Dengfeng
AU - MaCarthy, Susan A.
AU - Howe, Kerstin
AU - Durbin, Richard L.
AU - Wood, Jonathan
AU - Wang, Yadong
PY - 2020
DA - 2020/01/23
PB - Oxford University Press
SP - 2896-2898
IS - 9
VL - 36
PMID - 31971576
SN - 1367-4803
SN - 1367-4811
SN - 1460-2059
ER -
Cite this
BibTex (up to 50 authors)
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@article{2020_Guan,
author = {Dengfeng Guan and Susan A. MaCarthy and Kerstin Howe and Richard L. Durbin and Jonathan Wood and Yadong Wang},
title = {Identifying and removing haplotypic duplication in primary genome assemblies},
journal = {Bioinformatics},
year = {2020},
volume = {36},
publisher = {Oxford University Press},
month = {jan},
url = {https://doi.org/10.1093/bioinformatics/btaa025},
number = {9},
pages = {2896--2898},
doi = {10.1093/bioinformatics/btaa025}
}
Cite this
MLA
Copy
Guan, Dengfeng, et al. “Identifying and removing haplotypic duplication in primary genome assemblies.” Bioinformatics, vol. 36, no. 9, Jan. 2020, pp. 2896-2898. https://doi.org/10.1093/bioinformatics/btaa025.